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visualization of matrix summary from TRANSFAC
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18 months ago
F ♦ 3.4k
Iran

hello friend,

i export TRANSFAC result as a text file, do you know please how i can visualize this file to showing logo?

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Question was answered before: https://www.biostars.org/p/19039/

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thank you for your help

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this is a TRANSFAC output

Matrix Factor name Position (strand) Core score Matrix score Sequence
V$SRY_Q6 SRY 11 (-) 1.000 1.000 aAACAA
V$YY1_Q6_03 YY1 15 (-) 1.000 1.000 aaAATGG
V$NFAT1_Q4 NF-AT1 83 (-) 1.000 1.000 tTTTCC
V$RBPJK_01 RBP-Jkappa 84 (-) 1.000 0.935 ttTCCCAccaa
V$ING4_01 ING4 88 (+) 1.000 1.000 cCACCA
V$DMRT4_01 DMRT4 98 (+) 0.912 0.930 aatGTGTCaaaat
V$MZF1_Q5 MZF-1 127 (-) 1.000 1.000 cTCCCCa
V$SP100_04 SP100 secondary motif 132 (-) 1.000 0.959 cagttcttCGACGgc
V$NF1A_Q6_01 NF-1A 215 (+) 1.000 1.000 tGCCAAg
V$STAT1_Q6 STAT1 381 (-) 1.000 0.993 gTTCCCggaa
V$NFAT1_Q4 NF-AT1 450 (+) 1.000 1.000 GGAAAa
V$CRX_Q4_01 CRX 472 (-) 1.000 1.000 GATTAa
V$AML3_Q6 AML3 528 (-) 1.000 1.000 ttGTGGTt
V$ZNF333_01 ZNF333 655 (-) 1.000 1.000 ATTAT
V$RUSH1A_02 RUSH-1alpha 656 (-) 1.000 0.998 ttATAAGgat
V$ZNF333_01 ZNF333 664 (-) 1.000 1.000 ATTAT
V$ZNF333_01 ZNF333 748 (+) 1.000 1.000 ATAAT
V$HMGIY_Q3 HMGIY 755 (+) 1.000 0.948 ggtgtAATTTtataa
V$CDX2_Q5_02 CDX-2 763 (+) 1.000 1.000 TTTATa
V$ZNF333_01 ZNF333 766 (+) 1.000 1.000 ATAAT
V$SRY_Q6 SRY 793 (-) 1.000 1.000 aAACAA
V$HMGIY_Q3 HMGIY 797 (-) 1.000 0.963 aaaatAAATTgaagt
V$CDX2_01 Cdx-2 806 (+) 1.000 0.962 tgaagtaATAAAaggg
V$RFX_Q6 RFX 821 (+) 1.000 0.984 gtGTTGCcg
V$CDX2_01 Cdx-2 833 (-) 1.000 0.958 atatTTTATtgcttat

none of mentioned tools in above suggested link accept my daya as input, then how i can visualize above table as logoes please??

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What information would you need to draw a sequence logo? Does the file you have contain the information necessary to do so (it looks like it does not)?

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thank you Sean,

which i pasted above is the TRANSFAC's output that i want to visualize for my paper because there was not any option to save as logoes or anything, just there is an export file option.

today totally i was trying to create logoes but Weblogo rejects TRANSFAC output, Weblogo accepts fasta file but i could not find any fasta output in TRANSFAC

i am using free trail, today i noticed that fasta, match and more of options are inactive there

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I'm really not trying to NOT answer your question, but to lead you to think about what you are trying to do. I'm not asking what files you have or don't have. I'm asking what information you would need to draw a sequence logo. In other words, what data does a sequence logo display? Would one fasta sequence be enough, or would you need multiple? Alternatively, if you were to encode the information for a sequence logo as numbers, what might that look like?

https://en.wikipedia.org/wiki/Sequence_logo

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thank you Sean,your tips can clear some of my doubts...my free trial expired then i am going to use JASPAR embeded in a workbench which draws the logoes itself and i should to work more on the result interpretation.

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18 months ago
F ♦ 3.4k
Iran

Sarah, in free trial of TRANSFAC many of export options are deactive

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